Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PAF1

Cell type

Cell type Class
Digestive tract
Cell type
HCT 116
Primary Tissue
Colon
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Isolated from the colon
cell line
HCT116
tissue
colon
treatment
DMSO for 6 hours
chip antibody
PAF1
geo_loc_name
missing
collection_date
missing

Sequenced DNA Library

library_name
GSM6721411
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Rx experiments were performed as previously described (Li et al., 2021; Wang et al., 2021). Briefly, 1×10^7 human cells were spiked-in with 1-2×10^6 MEF cells and were fixed with 1% paraformaldehyde in PBS for 10 minutes, and quenched with 0.125 M glycine for 5 minutes. Fixed cells were used for nuclei isolation and were sheared using the Diagenode Bruptor Plus with the high-power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). The chromatin was immunoprecipitated with 5 μg individual antibodies and 15 μL of pre-blocked Protein A/G beads (Santa Cruz, Cat# sc-2003). After wash for three times with wash buffer (50 mM HEPES-KOH at pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-Deoxycholate), the captured DNA was eluted and reverse-crosslinked with 200 μL of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS, 200 μg/mL proteinase K) by incubating at 55°C overnight. The DNA was purified by phenol-chloroform extraction and ethanol precipitation. library strategy: ChIP-seq-Rx Following HaloPROTAC3 treatment, cells were collected and lysed with Trizol reagent. Total RNA was extracted according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
19804377
Reads aligned (%)
76.9
Duplicates removed (%)
17.3
Number of peaks
850 (qval < 1E-05)

hg19

Number of total reads
19804377
Reads aligned (%)
76.5
Duplicates removed (%)
17.4
Number of peaks
758 (qval < 1E-05)

Base call quality data from DBCLS SRA